Thermodynamic insight into stimuli-responsive behaviour of soft porous crystals

Knowledge of the thermodynamic potential in terms of the independent variables allows to characterize the macroscopic state of the system. However, in practice, it is difficult to access this potential experimentally due to irreversible transitions that occur between equilibrium states. A showcase example of sudden transitions between (meta) stable equilibrium states is observed for soft porous crystals possessing a network with long-range structural order, which can transform between various states upon external stimuli such as pressure, temperature and guest adsorption. Such phase transformations are typically characterized by large volume changes and may be followed experimentally by monitoring the volume change in terms of certain external triggers. Herein, we present a generalized thermodynamic approach to construct the underlying Helmholtz free energy as a function of the state variables that governs the observed behaviour based on microscopic simulations. This concept allows a unique identification of the conditions under which a material becomes flexible

Thermodynamic insight in the high-pressure behavior of UiO-66: effect of linker defects and linker expansion

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal organic frameworks, including the pristine UiO-66 to-68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials

Dating the emergence of the divaricate habit in the New Zealand flora

The New Zealand divaricates are a collection of shrubs, short trees and tree juveniles whose crowns are made of tough interlaced twigs branching at wide angles and bearing small leaves. These species represent c. 13% of the native woody flora, a proportion not seen in any other region of the world. Since the late 19ᵗʰ century, ecologists and botanists have sought to understand the of drivers this unique case of convergent evolution. Debate has been dominated by two main competing hypotheses invoking (1) the effect of browsing by now-extinct avian herbivores (moa) and (2) a response to frosty and droughty Plio-Pleistocene climates. Observational and experimental evidence, as well as theoretical discussions, have not clearly favoured one over the other. More recently, a synthetic hypothesis involving both climate and browsing has been proposed, but has not been specifically tested yet: the divaricate habit did not become advantageous as an anti-browsing defence until Plio-Pleistocene climatic constraints prevented young trees and shrubs from growing quickly out of reach of ground-dwelling herbivores. These hypotheses imply different expected divergence periods between divaricate species and their non-divaricate relatives. The focus of this PhD project is to produce a dated phylogeny including as many divaricates as possible, with the aim of bringing new evidence to help tease apart the various hypotheses about their evolution. This PhD thesis is built from a previously published paper and draft manuscripts intended for submission to scientific journals. The first two papers report phylogenies of small genera (Pennantia J.R.Forst. & G.Forst. and Corokia A.Cunn.) that include divaricate species. These studies helped develop lab methods and offered the opportunity to test diverse phylogenetic methods on a smaller scale in preparation for the third paper, which is the core dating work of this PhD. The phylogenies of Pennantia and Corokia provided in this thesis (Chapter 2 and 3, respectively) are the first published dated phylogenies of all the species of each genus. Building the phylogeny of Corokia was also the occasion to discuss two theories trying to explain the distribution of extant species on landmasses formerly part of Gondwana: vicariance and long-distance dispersal—Corokia appears to be one of an increasing number of cases where long-distance dispersal is indicated. The dated phylogeny of most New Zealand divaricate species presented in Chapter 4 reveals that, in the great majority of genera with divaricate representatives, the divaricate habit appeared in New Zealand within the last 5 My, i.e. since the beginning of the Pliocene. On one hand, this research constitutes a valuable methodological addition to the field of molecular phylogenetics by (1) disseminating a method for retrieving extra genetic markers, at no marginal cost, from Next Generation Sequencing shotgun sequencing data of DNA samples enriched for a specific set of markers, and (2) developing a guide to using a piece of phylogenetic reconstruction software (treePL), which was missing from the literature and needed by users. On the other hand, dating the emergence of the divaricate habit brought new and crucial evidence to the debate over what promoted the evolution of the divaricate habit in New Zealand: the findings are clearly consistent with a major effect of Plio-Pleistocene climates—and given evidence and discussion from past studies of these plants and similar plants around the world, the effect of browsing by moa was also probably involved

Préface

Cet ouvrage est avant tout l'analyse et l'interprétation d'un dossier épigraphique consistant confronté au départ, à l'aube de l'Empire, à la liste brève et d'interprétation souvent délicate donnée par Pline l'Ancien dans le livre V de l'Histoire Naturelle

A comparison of barostats for the mechanical characterization of metal-organic frameworks

In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterize closed pore the rigid MOF-5 and flexible MIL-53(Al) metal organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK), and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behavior in isothermal isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well-reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well-reproduced by any of the coupling schemes

Crystals springing into action : metal–organic framework CUK-1 as a pressure-driven molecular spring

Mercury porosimetry and in situ high pressure single crystal X-ray diffraction revealed the wine-rack CUK-1 MOF as a unique crystalline material capable of a fully reversible mechanical pressure-triggered structural contraction. The near-absence of hysteresis upon cycling exhibited by this robust MOF, akin to an ideal molecular spring, is associated with a constant work energy storage capacity of 40 J g(-1). Molecular simulations were further deployed to uncover the free-energy landscape behind this unprecedented pressure-responsive phenomenon in the area of compliant hybrid porous materials. This discovery is of utmost importance from the perspective of instant energy storage and delivery

The Atacama Cosmology Telescope: Two-Season ACTPol Lensing Power Spectrum

We report a measurement of the power spectrum of cosmic microwave background (CMB) lensing from two seasons of Atacama Cosmology Telescope Polarimeter (ACTPol) CMB data. The CMB lensing power spectrum is extracted from both temperature and polarization data using quadratic estimators. We obtain results that are consistent with the expectation from the best-fit Planck LCDM model over a range of multipoles L=80-2100, with an amplitude of lensing A_lens = 1.06 +/- 0.15 (stat.) +/- 0.06 (sys.) relative to Planck. Our measurement of the CMB lensing power spectrum gives sigma_8 Omega_m^0.25 = 0.643 +/- 0.054; including baryon acoustic oscillation scale data, we constrain the amplitude of density fluctuations to be sigma_8 = 0.831 +/- 0.053. We also update constraints on the neutrino mass sum. We verify our lensing measurement with a number of null tests and systematic checks, finding no evidence of significant systematic errors. This measurement relies on a small fraction of the ACTPol data already taken; more precise lensing results can therefore be expected from the full ACTPol dataset.Comment: 17 pages, 11 figures, to be submitted to Physical Review

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

We present a new measurement of the kinematic Sunyaev-Zeldovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zeldovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.Comment: 15 pages, 8 figures, 2 table

The Atacama Cosmology Telescope: The polarization-sensitive ACTPol instrument

The Atacama Cosmology Telescope (ACT) is designed to make high angular resolution measurements of anisotropies in the Cosmic Microwave Background (CMB) at millimeter wavelengths. We describe ACTPol, an upgraded receiver for ACT, which uses feedhorn-coupled, polarization-sensitive detector arrays, a 3 degree field of view, 100 mK cryogenics with continuous cooling, and meta material anti-reflection coatings. ACTPol comprises three arrays with separate cryogenic optics: two arrays at a central frequency of 148 GHz and one array operating simultaneously at both 97 GHz and 148 GHz. The combined instrument sensitivity, angular resolution, and sky coverage are optimized for measuring angular power spectra, clusters via the thermal Sunyaev-Zel'dovich and kinetic Sunyaev-Zel'dovich signals, and CMB lensing due to large scale structure. The receiver was commissioned with its first 148 GHz array in 2013, observed with both 148 GHz arrays in 2014, and has recently completed its first full season of operations with the full suite of three arrays. This paper provides an overview of the design and initial performance of the receiver and related systems